# The Conflicting classification of SCN5A p.Arg104Gln rests on one outdated submission, not on divided evidence

**Ethan Bradley**

Independent researcher, no institutional affiliation

ORCID: [0009-0008-8925-7975](https://orcid.org/0009-0008-8925-7975)

## Abstract

The ClinVar record for SCN5A p.Arg104Gln (NM_000335.5:c.311G>A; VCV000067780.15) currently reads "Conflicting classifications of pathogenicity," while the adjacent substitution at the identical residue, p.Arg104Trp (c.310C>T; VCV000067778.18), is Pathogenic/Likely pathogenic with no conflicts. I assembled the public evidence behind both records and find the conflict does not reflect a genuine split in the evidence. Of seven submitters who have applied classification criteria to R104Q, six call it Pathogenic or Likely pathogenic; the sole dissent, an Uncertain significance submission from a population-screening cohort last evaluated 6 October 2023, predates two calibrated functional datasets published in 2024 and 2025 (PMID 38953211, PMID 41251004). In those datasets R104Q and R104W are statistically indistinguishable on dominant-negative current and on automated patch-clamp Z-score. The identical substitution at the same invariant arginine is independently classified Pathogenic in SCN1A and in SCN2A. Reanalysis of a 2013 oocyte dataset (PMID 23805106) shows R104Q shifts inactivation and slows recovery while leaving activation untouched, a specific gating defect rather than simple loss of expression. The founding family described in the original 2001 report showed low penetrance, which weakens but does not erase the segregation evidence. A Bayesian points evaluation of ACMG/AMP criteria places R104Q at Likely pathogenic on two independent scoring routes and does not support Uncertain significance. This is an argument for review, not a completed reclassification, and I am not a diagnostic laboratory. I am a heterozygous carrier of this variant; that fact and its implications are addressed under competing interests below.

## A key to the terms used here

- **SCN5A** is the gene for the heart's main sodium channel; **Nav1.5** is the protein.
  **p.Arg104Gln**, or **R104Q**, means arginine at protein position 104 replaced by glutamine.
  **c.311G>A** describes the same change at the DNA level.
- **ClinVar** is the public database of variants and laboratory interpretations. A **VCV** accession
  identifies the record for a variant; an **SCV** accession identifies one laboratory's individual
  submission within it. This distinction matters here, because the argument is about one SCV.
- ClinVar classifications run **Pathogenic**, **Likely pathogenic**, **Uncertain significance**,
  **Likely benign**, **Benign**. **Conflicting** is not a separate finding but a label ClinVar applies
  automatically when submitters disagree, which is the point of this note.
- **ACMG/AMP criteria** are the standard rules for classifying variants, with codes such as **PS3** for
  supporting functional evidence. **ClinGen** maintains gene-specific versions of those rules.
- **Penetrance** is the proportion of carriers who actually develop the condition. Low penetrance means
  many carriers stay well, which affects how a variant is ascertained but not how damaging it is.
- **Brugada syndrome** is an inherited arrhythmia condition associated with reduced cardiac sodium
  current.
- **Patch clamp** is the electrical measurement of current through ion channels in a cell.
  **Automated patch clamp** does it at scale under one calibrated protocol, which is what makes
  variants measured on it comparable to each other.
- **Dominant-negative** means the variant copy interferes with the working copy, so the loss exceeds
  what one broken copy of two would cause.
- **Oocyte expression** means the channel was tested in a frog egg cell rather than a mammalian cell, an
  older method whose absolute numbers do not transfer cleanly to human heart.
- **Paralogues** are related genes from duplication. **SCN1A R101Q** and **SCN2A R102Q** are the
  equivalent substitutions at the equivalent position in two sibling genes.
- **VEP** is Ensembl's Variant Effect Predictor, a computational tool. **Z score** expresses a result in
  standard deviations from a reference mean.

## Why this record is worth a second look

SCN5A encodes Nav1.5, the principal cardiac sodium channel, and loss-of-function variants in it cause Brugada syndrome. A variant's ClinVar classification shapes what a patient and their relatives are told, and what cascade testing follows. R104Q sits at a residue where a second, chemically different substitution has already been resolved without controversy. That asymmetry is the whole reason for this note. My interest in the question is not abstract: I carry R104Q heterozygously and have a clinical diagnosis of Brugada syndrome, a fact disclosed in full under competing interests.

## Methods

All ClinVar data (VCV000067780.15, VCV000067778.18, VCV000068528, VCV000422127, and their constituent SCV records) were retrieved on 26 July 2026 via NCBI E-utilities esearch and esummary, with per-submitter assertions parsed directly from the VCV XML rather than transcribed from a summary page. Computational variant scores (AlphaMissense, REVEL, PolyPhen-2, SIFT) were retrieved on the same date from the Ensembl VEP REST service (rest.ensembl.org) against transcript ENST00000423572; the VEP release version is not recorded in my working notes. ClinGen's Criteria Specification Registry (cspec.genome.network) and Evidence Repository (erepo.clinicalgenome.org) were queried on 26 July 2026 to establish whether an SCN5A-specific expert-panel rule set exists. Literature searches used Europe PMC full-text search restricted to the BODY field, with the terms "R104Q" and "R104W" jointly, and separately combined with "reclassification" and "conflicting"; PubMed and PMC were used to retrieve the primary functional and clinical papers cited throughout. Statistical recomputation (two-sample z-tests and Welch t-tests on published means and standard errors) was done by hand from reported summary statistics; no statistical software version is recorded for this step, so I state that plainly rather than inventing one. ACMG/AMP evidence was combined using the Bayesian points implementation described by Tavtigian and colleagues in 2020 (thresholds: Pathogenic at 10 or more points, Likely pathogenic at 6 to 9, Uncertain at 0 to 5); full bibliographic detail for that source was not available to me beyond the author name and year.

## R104Q and R104W move together in every assay that has tested them side by side

Both variants replace the same arginine at codon 104 of Nav1.5, one changing c.311G>A to glutamine and the other c.310C>T to tryptophan. Supplementary Table 1 of O'Neill and colleagues (*Genet Med* 2022, PMID 35305865) measured both on the SyncroPatch 384PE platform, first alone and then co-expressed with a genomically integrated wild-type allele. Expressed alone, current is abolished for both: 0.4 ± 0.2% of wild type for R104Q (n=22) against 0.5 ± 0.2% for R104W (n=24), a difference of -0.1 percentage points (95% CI -0.65 to +0.45, p=0.72). Co-expressed with wild type, the two remain indistinguishable: 68.3 ± 6.1% for R104Q (n=34) against 69.6 ± 7.3% for R104W (n=43), a difference of -1.3 points (95% CI -19.9 to +17.3, p=0.89). Because the wild-type allele in this assay is introduced by Sleeping Beauty genomic integration rather than diluted by the variant allele, the paper's own no-interference baseline is 100%, not 50%; against that baseline R104Q falls short by 31.7 points (z=5.20) and R104W by 30.4 points (z=4.16), both past the study's dominant-negative threshold of 75%.

The equivalence here is tight enough to bound, not just fail to reject. For the heterozygous measurement, no difference larger than about 16.9 percentage points (90% CI) is consistent with the data, and a true difference of 26.7 points or more would have been detected at 80% power. For the homozygous measurement the corresponding bounds are ±0.57 and ±0.79% of wild type. The honest statement is that no difference is resolvable at this sample size, not that the variants are proven identical.

A second, largely independent dataset agrees. The Vandenberg laboratory at the Victor Chang Cardiac Research Institute submitted evidence-only functional records to ClinVar for both variants (SCV007294411 for R104Q and SCV007294674 for R104W, both created 11 January 2026), citing the multi-site validation of an automated patch-clamp assay (PMID 38953211) and its cohort-scale application (PMID 41251004). R104Q scores a Z of -6.07 and R104W a Z of -6.17 on a scale where -4 marks severe loss of function; the submitting laboratory recommended `PS3_strong` for both, identically.

Computational predictors place the two in the same bin as well. AlphaMissense scores 0.8685 for R104Q and 0.8831 for R104W, both inside the 0.792 to 0.905 band that the published SCN5A calibration maps to `PP3_supporting`. REVEL gives 0.967 and 0.950; PolyPhen-2 and SIFT call both damaging without a calibrated strength. None of this distinguishes the pair.

## The identical substitution at the same invariant arginine is Pathogenic in two other sodium channel genes

The residue is conserved outside SCN5A. SCN1A carries p.Arg101Gln (c.302G>A), classified Pathogenic in ClinVar (VCV000068528). SCN2A carries p.Arg102Gln (c.305G>A), also Pathogenic (VCV000422127). All three genes share the same nucleotide substitution, G>A, at the aligned invariant arginine. In an alignment of the nine human Naᵥ paralogue sequences, the residue is invariant at all nine positions; that count is my own, and the sequence source is not further specified in my working notes, so I flag it as this analysis's own computation rather than a cited figure.

The relevant framework for treating paralogue evidence this way, para-SAME as the paralogous analogue of ACMG PS1, was formalised and validated on the sodium-channel family by Brünger and colleagues (*Genome Biol* 2025, PMID 40624578), with positive likelihood ratios reported up to 13.0. I applied the criterion across the ClinVar pathogenic and likely-pathogenic missense variants available for the nine paralogues (5,559 variants) against a small internal answer key of variants with independent functional evidence of pathogenicity or benignity: R104Q, R104W, Y87C and F93S each recovered a para-SAME match, while R34C, Q90K and V125L, treated as benign controls, recovered none. That separation was complete on this small check set in both directions, which is encouraging but is a check on my own application of the method, not an external validation of it.

This line of evidence has a property the functional assays lack: it does not depend on interpreting current traces, expression systems, or baselines. SCN1A p.Arg101Gln and SCN2A p.Arg102Gln were classified by submitters with no connection to the SCN5A functional data or to each other. Its limits are real. SCN1A causes epilepsy, SCN2A causes epilepsy and autism, and SCN5A causes arrhythmia; para-SAME argues that the residue is intolerant of this substitution across the family, not that the diseases are equivalent. The two paralogue classifications are themselves expert judgements built on separate evidence bases, not independent experiments, and no SCN5A expert panel exists to weigh any of this (see below). Para-SAME contributes one criterion to an ACMG assessment; it does not reclassify anything by itself.

## A thirteen-year-old oocyte dataset shows a specific gating defect, not simply lost current

The only dedicated functional study of R104Q, Gütter and colleagues (*Front Physiol* 2013, PMID 23805106), recorded it in Xenopus oocytes and reported gating parameters that the newer automated patch-clamp datasets do not tabulate. Their Table 3 gives, for wild type against R104Q: mid-activation voltage of -33.5 ± 0.4 mV against -34.0 ± 0.8 mV, a difference of -0.5 mV that is not significant (z=0.56, p=0.58); mid-inactivation voltage of -71.2 ± 0.7 mV against -73.8 ± 0.5 mV, a difference of -2.6 mV that is significant (z=3.02, p=0.003); and recovery time constant of 3.8 ± 0.1 ms against 4.6 ± 0.1 ms, a difference of +0.8 ms that is strongly significant (z=5.66, p<0.001). These z-tests are my own recomputation from the published means and standard errors and agree with the paper's own significance calls.

Activation is untouched. Inactivation shifts hyperpolarising and recovery slows. Channels that reach the oocyte membrane, at 29 ± 2% of wild-type current, are functionally abnormal in a specific, not general, way. That is different information from the O'Neill current-density measurements and it strengthens the case that R104Q is a genuine loss-of-function allele rather than an artefact of one expression system. It comes with an important restriction: these are measurements of R104Q expressed alone, the homozygous-equivalent condition, not co-expressed with wild type. They show that a mutant channel reaching the membrane gates abnormally. They do not show that R104Q disturbs the gating of a co-expressed wild-type channel, which is what the dominant-negative mechanism in a heterozygous carrier would require.

The two expression systems also disagree sharply in magnitude: essentially zero current in HEK293 cells against 29% in oocytes. Two explanations are both consistent with the data as it stands, a single defect that happens to be more severe in mammalian cells, or two separate defects, one affecting trafficking or assembly and dominant in mammalian cells, and an intrinsic gating defect visible only in channels that do arrive at the oocyte membrane. Nothing in the public record distinguishes these, and I do not claim one over the other.

## The founding family had low penetrance, and that cuts both ways

A systematic search of full texts turned up a fourth independent pathogenicity assessment of R104Q that neither names the gene nor the variant in its title: Campuzano and colleagues (*Sci Rep* 2015, PMID 25608792) score it in body text as "previously reported associated with the disease, CM014904 (3 points), and with a deleterious effect in some studies (3 points). Positive familial segregation was identified in less than 4 relatives (2 points) but no in vivo studies were performed. In vitro studies showed a functional effect (2 points), and in silico analysis revealed four databases with damaging prediction (2 points)," for a total of 12 points, which the paper states indicates pathogenicity.

The HGMD accession CM014904 in that quotation, decoded by the format convention that encodes a first-report year rather than accessed directly in the database, points to the original description of the variant, Levy-Nissenbaum and colleagues (*Genet Test* 2001, PMID 11960580). Reading that source directly rather than relying on the 2015 summary matters, because its abstract states plainly that "the families of these patients are characterized by a small number of symptomatic members" and that "low penetrance is probably the cause for the small number of symptomatic members in the two families positive for the SCN5A mutations." The 2015 note's "positive familial segregation in less than 4 relatives" describes weak segregation, and the 2001 source explains why: the founding family itself had low penetrance. Carrying R104Q is evidently not equivalent to certain disease, and PP1-type segregation evidence here should be weighted with that in mind rather than treated as strong support on its own. I have not read the primary relative-by-relative segregation counts, since the 2001 paper's full text was not accessible to me, and I am not asserting a specific number of affected relatives beyond what the 2015 paper's summary states.

This also offers a plausible, but unconfirmed, reading of the single dissenting ClinVar submission. That submission comes from the All of Us Research Program, a population-screening cohort rather than a clinical referral laboratory. A low-penetrance variant ascertained in an unselected population is exactly the setting where a population-screening submitter might reach a different conclusion than clinical laboratories seeing symptomatic probands, an ascertainment difference rather than a disagreement about the strength of the functional or paralogue evidence. I present this as a plausible inference, not an established fact, since the submitter's internal reasoning is not published.

The same 2001 paper also reports "a possible R34C polymorphism in two unrelated controls," an independent confirmation from the primary clinical literature that R34C, used above as a benign paralogue control, was indeed seen in unaffected individuals.

## The dominant-negative assay's own no-interference controls are not at 100%

Every dominant-negative statement above compares heterozygous current to an assumed baseline of 100%, one wild-type allele producing the full reference current with a dead mutant allele adding nothing. That assumption is testable against the 51 variants in the O'Neill 2022 dataset that have both homozygous and heterozygous measurements. Four of them are complete loss of function alone (homozygous current below 10% of wild type) yet show no dominant-negative effect when co-expressed: W822X (homozygous 4.7%, heterozygous 134.2 ± 5.2%, n=164), G1661R (5.6%, 112.0 ± 9.4%, n=44), S1672Y (1.0%, 100.8 ± 8.7%, n=47), and R893C (8.2%, 76.8 ± 10.8%, n=52), with a mean of 106.0% and standard deviation of 23.9% across the four. W822X, a nonsense variant truncated early enough that it cannot plausibly assemble into a multimeric complex, sits at 134.2%, 6.6 standard errors above the paper's assumed null of 100%.

Restating R104Q's effect against these alternative baselines changes its apparent size. Against the paper's own convention of 100%, R104Q falls short by 31.7 percentage points. Against the median of the four non-interfering controls, 106.4%, the shortfall is 38.1 points. Against the truncation control W822X alone, 134.2%, it is 65.9 points. The direction of the effect does not change under any baseline, and the comparison between R104Q and R104W is unaffected, since both share whatever baseline applies. What changes is the size of the claim: R104Q's dominant-negative effect is real but its magnitude sits somewhere between roughly 32 and 66 percentage points, with the range dominated by uncertainty in the assay's own baseline rather than by measurement noise on R104Q itself. I checked whether the paper's 75% dominant-negative threshold needs revision in light of this: only 2 of the 51 paired variants fall in the 75 to 106% window, and both, S1672Y and R893C, are among the four variants used to derive the 106% baseline in the first place, so that check is close to circular and has negligible practical effect on the study's published classifications. I record it rather than dropping it because the reasoning looked promising before the check showed otherwise.

## Has this argument already been made in print

Europe PMC full-text search on the BODY field for "R104Q" and "R104W" jointly returns exactly one publication, Gütter 2013, which characterised R104Q functionally but performed no co-expression experiment and no classification analysis, and predates all of the dominant-negative and automated patch-clamp data discussed above. Searches combining "R104Q" with "reclassification" or "conflicting" return nothing relevant. The main text of the 2025 Eur Heart J paper (PMID 41251004) does not mention residue 104. That paper's supplementary tables S1 through S9 are behind a subscription and I could not open them. It is possible that R104Q already appears in one of those tables with a proposed classification; if so, this note would be corroboration rather than a new observation, and that possibility should be checked by anyone with access before this argument is treated as novel. I flag this honestly as an open question I could not resolve, not as a settled negative.

## What this adds up to under ACMG/AMP criteria

No SCN5A-specific expert-panel rule set exists to arbitrate any of this. The ClinGen Criteria Specification Registry held 206 specifications across 189 genes and 65 Variant Curation Expert Panels as of 26 July 2026, and none covers SCN5A; the only cardiac-rhythm specification available is for KCNQ1, an RYR2 panel is not yet released, and the five sodium-channel specifications that do exist (SCN1A, SCN2A, SCN3A, SCN8A, SCN1B, all from the Epilepsy Sodium Channel VCEP) do not apply to a cardiac channel. The ClinGen Evidence Repository confirms the same absence while returning records for KCNQ1, MYH7 and CDH1, so this is a true gap rather than a query failure. Generic ACMG/AMP criteria apply, informed by the assay-specific calibration published alongside the functional data.

Under the SVI framework for PS3/BS3 (Brnich and colleagues, *Genome Med* 2019, PMID 31892348), evidence strength is tied to a calibrated OddsPath, with thresholds of 2.1 for supporting, 4.3 for moderate, 18.7 for strong, and 350 for very strong. The SCN5A-Brugada automated patch-clamp assay was calibrated against 49 controls (25 benign, 24 pathogenic), reaching 96% sensitivity, 96% specificity, and an OddsPath of 24.0 in the pathogenic direction (PMID 38953211), above the strong threshold. R104Q's Z-score of -6.07 sits well inside the severe bin the assay defines, and neither R104 variant was among the calibration controls, so `PS3_strong` applies without circularity.

R104W is a different missense change at the same residue with a clean Pathogenic/Likely pathogenic classification, which would ordinarily support `PM5`. The concern is double-counting if R104W's status rested on the same assay: it does not, since six of R104W's seven classifying submissions were evaluated between 2020 and May 2024, before the assay's August 2024 publication, so its status rests on clinical evidence gathered independently. `PM5` applies at moderate strength; a curator who prefers strict independence may withhold it without changing the final bin (below). `PM2_supporting` applies because the ClinVar record reports a gnomAD exomes allele frequency of 0.00000 for R104Q, below the filtering threshold of 0.00003 used in the SCN5A-Brugada scheme; the gnomAD version behind that figure is not recorded in my source material. `PP3_supporting` applies on the AlphaMissense score described above, and should not be taken above supporting.

Several criteria that might seem applicable are not. `PS4` is not met: R104Q appears in 3 Brugada cases in the Walsh cohort, below the threshold of 5 needed for `PS4_supporting`. `PS2`/`PM6` do not apply, since no de novo occurrence is documented and, in my own case, the variant is inherited rather than de novo. `PP1` is withheld, because the Campuzano and Levy-Nissenbaum sources describe segregation in fewer than four relatives without giving the primary counts, and because the low-penetrance character of the founding family weakens what that segregation evidence would otherwise support. `PVS1` does not apply, since this is a missense change regardless of how completely it abolishes current. `PM1` is withheld, since the published scheme's N-terminal hotspot bonus depends on frequency and ancestry conditions I cannot verify for this variant from the public record. None of `BS3`, `BP4`, or `BS1` apply, since every line of evidence runs in the pathogenic direction.

Combining these with the Bayesian points implementation (Pathogenic at 10 or more, Likely pathogenic at 6 to 9, Uncertain at 0 to 5): with PM5 included, `PS3_strong` (4) plus `PM5` (2) plus `PM2_supporting` (1) plus `PP3_supporting` (1) totals 8, Likely pathogenic. Without PM5, the total is 6, still Likely pathogenic. Neither route reaches Pathogenic without additional clinical evidence such as verified segregation or stronger case enrichment, and I have not attempted to fold the SCN1A/SCN2A paralogue evidence into this points total, since none of my source material carries a worked Bayesian score that includes it; adding a PS1-strength code to an already Likely-pathogenic total would plausibly move the variant further, but I report that as an implication rather than a number I can verify. On either scored route, Uncertain significance is not supported by the evidence I could assemble.

## The current shape of the ClinVar record

As retrieved on 26 July 2026, both VCV records carry nine submissions from nine submitters, seven of which apply classification criteria in each case. For R104Q (VCV000067780.15): Pathogenic from Labcorp Genetics (SCV000291795.7, 2025-09-30), Women's Health and Genetics/LabCorp (SCV005380503.1, 2024-08-20), the Montreal Heart Institute laboratory (SCV006065867.1, 2024-02-05), and Skåne University Hospital Lund (SCV005198180.1, 2023-09-19); Likely pathogenic from Ambry Genetics (SCV006422169.1, 2025-08-15) and GeneDx (SCV000235319.12, 2025-03-04); and Uncertain significance from the All of Us Research Program (SCV004834939.1, 2023-10-06). That is four Pathogenic, two Likely pathogenic, one Uncertain. For R104W (VCV000067778.18): Pathogenic from Labcorp Genetics (SCV002292504.5, 2026-01-07), Victorian Clinical Genetics Services (SCV005400264.1, 2023-07-17), Women's Health and Genetics/LabCorp (SCV004020423.1, 2023-06-12), the University of Leipzig laboratory (SCV003925662.1, 2023-04-19), and Ambry Genetics (SCV000738139.5, 2020-09-22); Likely pathogenic from GeneDx (SCV000518408.5, 2024-05-24) and Fulgent Genetics (SCV002800405.1, 2021-07-13). Five Pathogenic, two Likely pathogenic, no conflicts.

Four laboratories have classified both variants. Labcorp Genetics calls both Pathogenic. Women's Health and Genetics/LabCorp calls both Pathogenic. GeneDx calls both Likely pathogenic. Ambry Genetics calls R104W Pathogenic and R104Q Likely pathogenic, a real difference of one step that should be stated rather than smoothed over, but it is a difference between two pathogenic categories, not between pathogenic and uncertain. No laboratory that has classified both variants places R104Q in the uncertain category. The aggregate discrepancy in ClinVar's summary label is produced entirely by the single All of Us submission. Remove it, and R104Q's composition, four Pathogenic and two Likely pathogenic, closely matches R104W's five Pathogenic and two Likely pathogenic, with no conflict in either case. The dissenting submission cites "ACMG Guidelines, 2015" and was last evaluated on 6 October 2023, before the assay validation published in August 2024 (PMID 38953211), before the cohort-scale application published in November 2025 (PMID 41251004), and before the R104Q functional record itself was deposited in ClinVar in January 2026. A submission predating the evidence it would need to weigh is the ordinary reason a classification becomes outdated, not evidence of an unresolved scientific disagreement.

## What would change my mind about this argument

Several specific findings would weaken or overturn what I have argued here. If the Eur Heart J 2025 supplementary tables, once accessible, show that R104Q has already been evaluated and placed in a category inconsistent with the argument above, that evaluation should take precedence over this note. If an independent laboratory using a different platform than SyncroPatch 384PE, and without shared senior authorship with the O'Neill and Ma groups, measured R104Q and R104W and found a real difference between them, the central claim of functional equivalence would need to be withdrawn. If the primary relative-by-relative segregation data in the 2001 Levy-Nissenbaum paper, once read directly, showed segregation inconsistent with a low-penetrance interpretation, the reading given here would need revision. If the All of Us submitter's internal reasoning were disclosed and showed genuine disagreement with the functional or paralogue evidence rather than an ascertainment difference, the reframing offered above would not hold. If co-expression data in a mammalian system showed that R104Q's oocyte gating defect disappears when the variant is expressed alongside wild type, that would separate the mechanism described here from the dominant-negative phenotype actually seen in heterozygous carriers, which is the discriminating experiment this note cannot itself perform.

## What this note does not claim

This is an argument that a specific ClinVar submission should be reviewed against evidence published after it was made. It is not a reclassification, and I have no authority to issue one. I am not a clinical diagnostic laboratory, I have not examined any patient, and nothing in this note constitutes clinical advice or a diagnosis for any individual, including myself. Classification decisions for this or any variant belong to a qualified clinical genetics laboratory applying its own validated procedures, and any question about what a given classification means for a specific person's care belongs with that person's own treating clinicians and genetic counselors, not with this document.

## Data availability

All primary data used here are public. ClinVar records: VCV000067780.15 (R104Q), VCV000067778.18 (R104W), VCV000068528 (SCN1A R101Q), VCV000422127 (SCN2A R102Q), and the constituent SCV records named throughout, retrieved via NCBI E-utilities. Functional data: O'Neill et al., *Genet Med* 2022, PMID 35305865, Supplementary Table 1 (also available as bioRxiv doi:10.1101/2021.09.22.461398, Table S1); Ma et al., *Circ Genom Precis Med* 2024, PMID 38953211; O'Neill et al., *Eur Heart J* 2025, PMID 41251004, doi:10.1093/eurheartj/ehaf874; Gütter et al., *Front Physiol* 2013, PMID 23805106, Table 3. Clinical and segregation data: Campuzano et al., *Sci Rep* 2015, PMID 25608792; Levy-Nissenbaum et al., *Genet Test* 2001, PMID 11960580. Computational scores: Ensembl VEP REST (rest.ensembl.org) on transcript ENST00000423572. Framework references: Brnich et al., *Genome Med* 2019, PMID 31892348; Brünger et al., *Genome Biol* 2025, PMID 40624578. Registry checks: ClinGen Criteria Specification Registry (cspec.genome.network) and Evidence Repository (erepo.clinicalgenome.org), both accessed 26 July 2026. All derived tables are deposited as a single archive with a permanent identifier. The identifier is
recorded in DATA_DOI.txt alongside this manuscript and should be cited as the data source. They comprise the recomputed statistics, the paralogue alignment counts, and the baseline-recalibration figures.

## Competing interests

I am a heterozygous carrier of SCN5A p.Arg104Gln, the variant discussed in this note, and I have a clinical diagnosis of Brugada syndrome.

## References

1. O'Neill MJ, Muhammad A, Li B, Wada Y, Hall L, Solus JF, Short L, Roden DM, Glazer AM. Dominant negative effects of SCN5A missense variants. Genet Med. 2022;24:1238-1248. PMID 35305865.
2. Ma JG, O'Neill MJ, Richardson E, Thomson KL, et al., Glazer AM, Ng CA. Multisite validation of a functional assay to adjudicate SCN5A Brugada syndrome-associated variants. Circ Genom Precis Med. 2024;17:e004569. PMID 38953211.
3. O'Neill MJ, Ma JG, Aldridge JL, Solus JF, et al., Glazer AM, Ng CA. Automated patch clamp data improve variant classification and penetrance stratification for SCN5A-Brugada syndrome. Eur Heart J. 2025. PMID 41251004. doi:10.1093/eurheartj/ehaf874.
4. Gütter C, Benndorf K, Zimmer T. Characterization of N-terminally mutated cardiac Na+ channels associated with long QT syndrome 3 and Brugada syndrome. Front Physiol. 2013. PMID 23805106.
5. Campuzano O, Sarquella-Brugada G, Cesar S, et al. Determining the pathogenicity of genetic variants associated with cardiac channelopathies. Sci Rep. 2015. PMID 25608792.
6. Levy-Nissenbaum E, Eldar M, Wang Q, et al. Genet Test. 2001;5(4):331-334. PMID 11960580.
7. Brnich SE, Abou Tayoun AN, Couch FJ, et al. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med. 2019;12:3. PMID 31892348.
8. Brünger T, et al. Paralogue-based variant interpretation in ion channel genes. Genome Biol. 2025. PMID 40624578.
9. Tavtigian et al., 2020 (Bayesian points implementation of the ACMG/AMP classification framework; full bibliographic details not available in my source material).